pcaMethods not loading with missCompare library

[kieroneil]

I was going to walk through the complete tutorial and ran into issues immediately.
> library(missCompare)
Error: package or namespace load failed for ‘missCompare’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
there is no package called ‘pcaMethods’
In addition: Warning message:
package ‘missCompare’ was built under R version 3.5.3
> cleaned <- missCompare::clean(clindata_miss, var_removal_threshold = 0.5, ind_removal_threshold = 0.8, missingness_coding = -9)
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) :
there is no package called ‘pcaMethods’
> install.packages("pcaMethods")
Installing package into ‘C:/Users/koneil/Documents/R/win-library/3.5’
(as ‘lib’ is unspecified)
Warning in install.packages :
package ‘pcaMethods’ is not available (for R version 3.5.1)
> devtools::install_github("hredestig/pcaMethods")
Downloading GitHub repo hredestig/pcaMethods@master
Error: Could not find tools necessary to compile a package
In addition: Warning messages:
1: In untar2(tarfile, files, list, exdir) :
skipping pax global extended headers
2: In untar2(tarfile, files, list, exdir) :
skipping pax global extended headers

I ended up downloading a lot of build tools and got the same error message and decided to abandon.

It looks like a useful package for missing values. I'll re-try once the pcaMethods issue has been resolved.

[Tirgit]

Hi kieroneil,

Could you try two things?

1. Not sure which R version you are using, but make sure you use R>3.5.0 (although perhaps you should upgrade to 3.6.0)
2. Can you try install pcaMethods from Bioconductor first?
   Here is how you would do it:
   if (!requireNamespace("BiocManager", quietly = TRUE))
   install.packages("BiocManager")
   BiocManager::install("pcaMethods")

see more info here: https://www.bioconductor.org/packages/release/bioc/html/pcaMethods.html

Please let me know if these worked for you!
T